Re: [gmx-users] GPU problem with running gromacs.2018
Hi, When I send the full log I received this mail from the list. - Your mail to 'gromacs.org_gmx-users' with the subject Re: [gmx-users] GPU problem with running gromacs.2018 Is being held until the list moderator can review it for approval. The reason it is being held: Message body is too big: 60010 bytes with a limit of 50 KB Either the message will get posted to the list, or you will receive notification of the moderator's decision. If you would like to cancel this posting, please visit the following URL: https://maillist.sys.kth.se/mailman/confirm/gromacs.org_gmx-users/1 29a1575b806c54484b39d65032d5862b41be235 -- -Original Message- From: Szilárd Páll <pall.szil...@gmail.com> Reply-to: gmx-us...@gromacs.org To: Discussion list for GROMACS users <gmx-us...@gromacs.org> Subject: Re: [gmx-users] GPU problem with running gromacs.2018 Date: Fri, 16 Feb 2018 20:06:05 +0100 Hi, Indeed, this is an issue introduced in the 2018 release which aborts mdrun if an error is encountered during GPU detection; My first guess is that one of your GPUs is in exclusive or prohibited mode. You can use mdrun by skipping that GPU, i.e. setting the CUDA_VISIBLE_DEVICES environment variable. BTW, what you shared is not your full log! It would have been (and will be in the future) helpful if you actually shared the _full_ log file so we get all information not just what you find useful to paste in your reply; in this particular case seeing the hardware detection report would have helped a bit. Cheers, -- Szilárd On Fri, Feb 16, 2018 at 1:55 PM, Osmany Guirola Cruz <osmany.guir...@biocomp.cigb.edu.cu> wrote: > This is the output with gromacs 2018 and cuda 9 > - > --Program: gmx > mdrun, version 2018Source file: src/gromacs/gpu_utils/gpu_utils.cu > (line 735)Function:void findGpus(gmx_gpu_info_t*) > Assertion failed:Condition: cudaSuccess == > cudaPeekAtLastError()Should > be cudaSuccess > For more information and tips for troubleshooting, please check the > GROMACSwebsite at http://www.gromacs.org/Documentation/Errors > -- > - > > and this is the log > Log file opened on Fri Feb 16 07:49:19 2018Host: draco pid: > 20855 rank ID: 0 number of ranks: 1 :-) > GROMACS - gmx mdrun, 2018 (-: > GROMACS is written by: Emile > Apol Rossen Apostolov Herman J.C. BerendsenPar > BjelkmarAldert van Buuren Rudi van Drunen Anton > FeenstraGerrit Groenhof Christoph Junghans Anca > HamuraruVincent Hindriksen Dimitrios KarkoulisPeter > KassonJiri Kraus Carsten Kutzner Per Larsson > Justin A. LemkulViveca LindahlMagnus Lundborg Pieter > MeulenhoffErik Marklund Teemu Murtola Szilard > Pall Sander Pronk Roland Schulz Alexey > Shvetsov Michael Shirts Alfons Sijbers Peter > TielemanTeemu Virolainen Christian WennbergMaarten > Wolf and the project > leaders:Mark > Abraham, Berk Hess, Erik Lindahl, and David van der Spoel > Copyright (c) 1991-2000, University of Groningen, The > Netherlands.Copyright (c) 2001-2017, The GROMACS development team > atUppsala University, Stockholm University andthe Royal Institute of > Technology, Sweden.check out http://www.gromacs.org for more > information. > GROMACS is free software; you can redistribute it and/or modify > itunder > the terms of the GNU Lesser General Public Licenseas published by the > Free Software Foundation; either version 2.1of the License, or (at > your > option) any later version. > GROMACS: gmx mdrun, version > 2018Executable: /usr/local/gromacs/bin/gmxData > prefix: /usr/local/gromacsWorking > dir: /home/osmany/Downloads/RASCommand line: gmx mdrun -deffnm md > GROMACS version:2018Precision: singleMemory > model: 64 bitMPI library:thread_mpiOpenMP > support: enabled (GMX_OPENMP_MAX_THREADS = 64)GPU > support:CUDASIMD instructions: SSE4.1FFT > library:fftw- > 3.3.7-sse2-avxRDTSCP usage: disabledTNG > support:enabledHwloc support: hwloc-1.11.6Tracing > support:disabledBuilt on: 2018-02-14 14:05:11Built > by: osmany@draco [CMAKE]Build OS/arch: Linux 4.14.0-3- > amd64 x86_64Build CPU vendor: IntelBuild CPU brand:Intel(R) > Core(TM)2 Quad CPUQ9650 @ 3.00GHzBuild CPU family: 6 Model: > 23 Stepping: 10Build CPU features: apic clfsh cmov cx8 cx16 intel > lahf mmx msr pdcm pse sse2 sse3 sse4.1 ssse3C > compiler: /usr/bin/gcc-6 GNU 6.4.0C compiler flags
Re: [gmx-users] GPU problem with running gromacs.2018
This is the output with gromacs 2018 and cuda 9 ---Program: gmx mdrun, version 2018Source file: src/gromacs/gpu_utils/gpu_utils.cu (line 735)Function:void findGpus(gmx_gpu_info_t*) Assertion failed:Condition: cudaSuccess == cudaPeekAtLastError()Should be cudaSuccess For more information and tips for troubleshooting, please check the GROMACSwebsite at http://www.gromacs.org/Documentation/Errors-- - and this is the log Log file opened on Fri Feb 16 07:49:19 2018Host: draco pid: 20855 rank ID: 0 number of ranks: 1 :-) GROMACS - gmx mdrun, 2018 (-: GROMACS is written by: Emile Apol Rossen Apostolov Herman J.C. BerendsenPar BjelkmarAldert van Buuren Rudi van Drunen Anton FeenstraGerrit Groenhof Christoph Junghans Anca HamuraruVincent Hindriksen Dimitrios KarkoulisPeter KassonJiri Kraus Carsten Kutzner Per Larsson Justin A. LemkulViveca LindahlMagnus Lundborg Pieter MeulenhoffErik Marklund Teemu Murtola Szilard Pall Sander Pronk Roland Schulz Alexey Shvetsov Michael Shirts Alfons Sijbers Peter TielemanTeemu Virolainen Christian WennbergMaarten Wolf and the project leaders:Mark Abraham, Berk Hess, Erik Lindahl, and David van der Spoel Copyright (c) 1991-2000, University of Groningen, The Netherlands.Copyright (c) 2001-2017, The GROMACS development team atUppsala University, Stockholm University andthe Royal Institute of Technology, Sweden.check out http://www.gromacs.org for more information. GROMACS is free software; you can redistribute it and/or modify itunder the terms of the GNU Lesser General Public Licenseas published by the Free Software Foundation; either version 2.1of the License, or (at your option) any later version. GROMACS: gmx mdrun, version 2018Executable: /usr/local/gromacs/bin/gmxData prefix: /usr/local/gromacsWorking dir: /home/osmany/Downloads/RASCommand line: gmx mdrun -deffnm md GROMACS version:2018Precision: singleMemory model: 64 bitMPI library:thread_mpiOpenMP support: enabled (GMX_OPENMP_MAX_THREADS = 64)GPU support:CUDASIMD instructions: SSE4.1FFT library:fftw- 3.3.7-sse2-avxRDTSCP usage: disabledTNG support:enabledHwloc support: hwloc-1.11.6Tracing support:disabledBuilt on: 2018-02-14 14:05:11Built by: osmany@draco [CMAKE]Build OS/arch: Linux 4.14.0-3- amd64 x86_64Build CPU vendor: IntelBuild CPU brand:Intel(R) Core(TM)2 Quad CPUQ9650 @ 3.00GHzBuild CPU family: 6 Model: 23 Stepping: 10Build CPU features: apic clfsh cmov cx8 cx16 intel lahf mmx msr pdcm pse sse2 sse3 sse4.1 ssse3C compiler: /usr/bin/gcc-6 GNU 6.4.0C compiler flags:- msse4.1 -O3 -DNDEBUG -funroll-all-loops -fexcess- precision=fast C++ compiler: /usr/bin/g++-6 GNU 6.4.0C++ compiler flags: -msse4.1-std=c++11 -O3 -DNDEBUG -funroll-all- loops -fexcess-precision=fast CUDA compiler: /usr/lib/nvidia- cuda-toolkit/bin/nvcc nvcc: NVIDIA (R) Cuda compiler driver;Copyright (c) 2005-2017 NVIDIA Corporation;Built on Fri_Sep__1_21:08:03_CDT_2017;Cuda compilation tools, release 9.0, V9.0.176CUDA compiler flags:-gencode;arch=compute_30,code=sm_30;- gencode;arch=compute_35,code=sm_35;- gencode;arch=compute_37,code=sm_37;- gencode;arch=compute_50,code=sm_50;- gencode;arch=compute_52,code=sm_52;- gencode;arch=compute_60,code=sm_60;- gencode;arch=compute_61,code=sm_61;- gencode;arch=compute_70,code=sm_70;- gencode;arch=compute_70,code=compute_70;-use_fast_math;- D_FORCE_INLINES;; ;-msse4.1;-std=c++11;-O3;-DNDEBUG;-funroll-all- loops;-fexcess-precision=fast;CUDA driver:9.0CUDA runtime: 9.0 -- Osmany -Original Message-From: Szilárd Páll <pall.szil...@gmail.com>Re ply-to: gmx-users@gromacs.orgTo: Discussion list for GROMACS users Subject: Re: [gmx-users] GPU problem with running gromacs.2018Date: Thu, 15 Feb 2018 18:23:05 +0100 Please provide a full log file output.--Szilárd On Thu, Feb 15, 2018 at 6:11 PM, Osmany Guirola Cruz<osmany.guirola@bio comp.cigb.edu.cu> wrote: > Hi > > I am having problems running mdrun command compiled with GPU > support(cuda 9.0). > here is the output of the mdrun command > > > Using 1 MPI thread > Using 4 OpenMP threads > > 1 compatible GPU is present, with ID 0 > 1 GPU auto-selected for this run. > Mapping of GPU ID to the 1 PP rank in this node: 0 > > > WARNING: Just caught a previously occurred CUDA error (no kernel > image > is available for execution on the device), will try to continue. > > > ---
Re: [gmx-users] GPU problem with running gromacs.2018
Yes, it is true, sorry, but I have problems with both. With version 2018 the error it's diferent. that's why i compiled an older version. Osmany -Original Message- From: Szilárd Páll <pall.szil...@gmail.com> Reply-to: gmx-us...@gromacs.org To: Discussion list for GROMACS users <gmx-us...@gromacs.org> Subject: Re: [gmx-users] GPU problem with running gromacs.2018 Date: Thu, 15 Feb 2018 18:23:51 +0100 PS: Also, what you pasted in here states "2016.4", but your subject claims version 2018 -- Szilárd On Thu, Feb 15, 2018 at 6:23 PM, Szilárd Páll <pall.szil...@gmail.com> wrote: > Please provide a full log file output. > -- > Szilárd > > > On Thu, Feb 15, 2018 at 6:11 PM, Osmany Guirola Cruz > <osmany.guir...@biocomp.cigb.edu.cu> wrote: > > Hi > > > > I am having problems running mdrun command compiled with GPU > > support(cuda 9.0). > > here is the output of the mdrun command > > > > > > Using 1 MPI thread > > Using 4 OpenMP threads > > > > 1 compatible GPU is present, with ID 0 > > 1 GPU auto-selected for this run. > > Mapping of GPU ID to the 1 PP rank in this node: 0 > > > > > > WARNING: Just caught a previously occurred CUDA error (no kernel > > image > > is available for execution on the device), will try to continue. > > > > > > --- > > Program: gmx mdrun, version 2016.4 > > Source file: src/gromacs/mdlib/nbnxn_cuda/nbnxn_cuda.cu (line 740) > > > > Fatal error: > > cudaFuncSetCacheConfig failed: invalid device function > > > > For more information and tips for troubleshooting, please check the > > GROMACS > > website at http://www.gromacs.org/Documentation/Errors > > ... > > > > > > Thanks. > > Osmany > > > > -- > > Gromacs Users mailing list > > > > * Please search the archive at http://www.gromacs.org/Support/Maili > > ng_Lists/GMX-Users_List before posting! > > > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > > > * For (un)subscribe requests visit > > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users > > or send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] GPU problem with running gromacs.2018
Hi I am having problems running mdrun command compiled with GPU support(cuda 9.0). here is the output of the mdrun command Using 1 MPI thread Using 4 OpenMP threads 1 compatible GPU is present, with ID 0 1 GPU auto-selected for this run. Mapping of GPU ID to the 1 PP rank in this node: 0 WARNING: Just caught a previously occurred CUDA error (no kernel image is available for execution on the device), will try to continue. --- Program: gmx mdrun, version 2016.4 Source file: src/gromacs/mdlib/nbnxn_cuda/nbnxn_cuda.cu (line 740) Fatal error: cudaFuncSetCacheConfig failed: invalid device function For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors ... Thanks. Osmany -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.